


Running to a New Home

by interdimensionalhitchhiker84



Category: Harry Potter - J. K. Rowling, Stargate - All Media Types, Stargate Atlantis
Genre: Ancient John Sheppard, Asexual Harry Potter, Asexual John Sheppard, Bisexual Rodney McKay, Canon-Typical Violence, Genius Harry Potter, Harry Potter Epilogue What Epilogue | EWE, Harry Potter Leaves the Wizarding World, Harry Potter was Adopted by Other(s), Language Barrier, M/M, Master of Death Harry Potter, Multi, Sentient Atlantis, Series Rewrite, Sort Of, The Ancient gene is magic, Timeline Shift, background Natasha/Maria Hill, coulda been mensa, hp timeline moved back a decade, mostly just that Harry was unofficially adopted by Natasha after fourth year, of sga not hp, there is marvel but it's very minimal
Language: English
Status: In-Progress
Published: 2020-05-28
Updated: 2020-10-06
Packaged: 2021-03-02 22:55:18
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 5
Words: 12,764
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/24414700
Author URL: https://archiveofourown.org/users/interdimensionalhitchhiker84/pseuds/interdimensionalhitchhiker84
Summary: Harry Potter loved flying from the moment he touched a broom.  Harry Potter hated being famous the moment he found out he was.  He could never settle for playing quidditch professionally while dodging cameras.  Or for being an auror and having to keep facing people who wanted him dead because of Voldemort.  He ran, he had enough help to become someone new, and he became a normal guy with a normal name who could fly and help people and just be happy.  And then he sat in a chair and he was special all over again.  At least this time the details about how special he was were classified.
Relationships: Rodney McKay/John Sheppard
Comments: 46
Kudos: 209





	1. Prologue--Sitting in a Chair

**Author's Note:**

> I'm not entirely sure if I'll finish this. I've very bad at finishing things. That said, I'm just planning to follow canon but throw in some magic and behind the scenes stuff which gives me good direction. So, if there's interest, I'll make a real big effort. Please show interest by commenting or by hitting me up at everyheartbesure on tumblr. (Most of the Natasha stuff is based on rps between me and @iskupleniye on tumblr.)

_Britain, 1942_

Albus Dumbledore had been known to wear a black cloak or even a coat on occasion, but more often than not, even his outerware was brightly-colored and patterned, and that, combined with his high-heeled boots, didn’t exactly help him blend in. So, of all the leaders of the non-military war efforts, he seemed to be the one who was found most frequently by those who were assigned to kill him. 

Children wielding poorly-aimed accidental magic weren’t the normal assassins. He was understandably caught off guard, but he couldn’t have retaliated with his normal zeal if he’d wanted to. Instead, he watched her carefully, only truly stepping in to stop her when the child nearly hurt herself.

Natasha had been trained her whole life for this. She was highly-effective, and the fact that her current target didn’t seem all that bothered by her attacks was terrifying.

“What you’re doing now is more likely to hurt you than me,” Albus said gently.

“I don’t matter,” she replied dismissively. Her teeth were clenched against the way her magic was beginning to feel _raw_ and _painful_ , like it was rippling under the surface of her skin, ready to just rip free of her. “ _You’re_ what matters.” The _mission_ was what mattered.

Her magic was practically swirling around her, and it was obvious that despite her age, the child had never been trained to work with a focus. Dumbledore now held his wand loosely in his hand, and he conjured a pair of armchairs before taking a seat. “A deep breath might be helpful here. I’m sure you already know my name, but I’m Albus Dumbledore. I’m a professor at a school of magic. I could help you, if you wished it. I think you probably matter very much.”

She glared, but did as he suggested and took a breath. Then she perched on the edge of the second seat, when her angry magic overwhelmed her again. She would be punished for this. Probably in a new, _creative_ way. “You don’t know anything about me. You can’t help me. It doen’t matte what I _wish_ because wishes are for children, and I am _not_ a child.”

Dumbledore watched her carefully over his glasses, then sat back a little. “Children born with magical ability need to be trained so they do not hurt themselves or others accidentally. While it appears you’ve been trained enough to prevent a complete loss of control from killing you, you would still benefit a great deal from a focus and tutoring in how to use it. That is why magical schools exist and why attendance is mandatory in most countries.”

“Pah, ‘of age,’” she repeated dismissively. “I’ve been _married_. I’ve- I’m not a child.” She said it again like she could make him believe it, though he so clearly now believed her to be something to be protected and nurtured. “I can’t just… go to a _school_. For _magic_. Even if I wanted to, do you think I just woke up and decided to be an assassin?” Her glare was cold, the tilt of her chin daring him to challenge her, though that would likely mean the end of her.

“Perhaps you deserve the chance to be, then,” he suggested. “It’s sad, when childhood ends so early. Of course, you don’t need to be a child to attend school.”

Albus took a deep breath, and then sighed, steepling his fingers under his chin and leaning forward to meet her eyes thoughtfully. “I could offer you protection. Schools for magic are not easily found or entered. It is a great stain on society whenever one is forced into a bloody profession one did not choose. When one is able to step away from that and become what they wish to be… I’d like to think it wipes away some of that stain.”

Perplexed, Natasha frowned. “I’ve been an assassin since I was ten years old. Don’t you think it’s a bit foolish to even consider being a child _now_?” She arched one brow in a look that typically intimidated far more frightening men than he. “I don’t wish to be anything else,” she lied painfully. “I’m a weapon. Weapons are to be used. Not for---not for learning, or any other foolish thing you might think I should be doing.” The idea of leaving—of going somewhere safe only to be trapped there—scared her terribly. She didn’t know who she was without being an assassin and a soldier and a spy in this bloody, awful war. It had been her whole life. A student? She hadn’t been that for several years, and before that… well. She didn’t think that Albus Dumbledore would have considered that a subject worth learning. 

“Even _if_ I wanted to go with you… they’d find me. That would put the _actual children_ at your school at risk.” She said it like a challenge, daring him to counter with platitudes that she couldn’t see how either of them could believe.

“What would life be without the chance to engage in some foolishness?” he responded with a soft smile and a hint of a twinkle. “I’m afraid, without formal education in controlling your ability, you might very well be putting _actual_ children in danger everywhere you go.” Dumbledore copied her inflection, despite his firm belief that she was still very much a child, as sad as her terrible experiences were. “Our children are the most important things in the world to us—to the magical community. Our school is protected so thoroughly that those not invited cannot even find it. You would not pose nearly the danger you believe, there.”

He paused for a long moment to let her absorb that, then pushed a little harder. “Perhaps you would let me teach you something simple now? Even a start is better than nothing at all.”

She was silent for a long moment, struggling to resist the temptation to kick something and prove him right about her level of maturity. “What do you want to teach me?” This man was truly magical, and despite her fear, he was offering realms of knowledge and control that her handlers had never—would never—give her. And she was so incredibly _weak_ that she couldn’t resist the temptation entirely.

That was exactly the start Dumbledore needed. She traveled to Hogsmead with him that night.

* * *

_Hogwarts, 1984_

The school had been swarming with guests since the arrival of the other schools’ delegations the day before. Some of them were clearly associated with one of the schools, some of them were obviously some kind of press, some of them were ministry officials or people who were involved in organizing the tournament, and some were just people. Friends or acquaintances of those who had already been invited who were along for the ride just to see how things played out. 

Natasha was one of those people. She had been in contact with Dumbledore since her teenage years during Grindlewald’s war, and she had come back to visit and see the excitement when the tournament was announced. She’d been hoping for a great deal more from it all than that poor child being given even more to deal with.

Albus had said, when he’d brought her here, that children were protected at all costs by this world. She’d come to believe it, in her time under his care. And yet, here they were, a child being forced to compete in a life-threatening competition against his will. She had never hated wizards more.

* * *

_Hogwarts, 1984_

A week before the first task, Natasha found Harry sitting alone in the stands around the quidditch pitch, looking both numb and terrified.

“Hello, Mr. Potter. I’m Natasha Romanova. I wanted you to know that I believe you didn’t enter this competition willingly and that I am appalled that you are being forced to compete. You don’t have to speak to me, but I was forced to do something terribly dangerous at your age, and that wasn’t alright. So, if you need anything—whether that’s an adult to listen to you and believe you, help with preparations, or chocolate to help you through the stress—anything at all,” she smiled reassuringly, “I want you to know that you’re welcome to reach out to me. I think I’ll be sticking around the school for a while.”

Harry wasn’t sure whether or not to believe her, but it wasn’t the only interaction he had with her that year.

* * *

_Kings Cross Station, 1985_

Harry was not looking forward to this summer. He did, at least, have the continued, flimsy protection of a godfather who was an escaped, convicted mass-murderer to scare his relatives, but he was too much of a mess after everything to care much. So, he was already looking thoroughly miserable when he stepped off the platform.

He was met with the shocking view of Sirius, barely disguised, Natasha, who’d easily been the kindest and most helpful adult he’d ever met, and his uncle, looking painfully uncomfortable. Sirius seemed to be glaring at Natasha as much as he was Vernon, which was odd because he didn’t know they’d even met. 

“Er… Miss Romanova? Is there something wrong?”

It was only years of practice that kept her from hexing everyone who was making this even more confusing for Harry. Tearing her gaze off Sirius and Vernon Dursley, she focused on Harry with a smile. “There’s not a problem exactly, Harry, but it’s been arranged so that you’ll come and stay with me, this summer at the very least. And there’s, ah, some disagreement over that. What do you think of the idea?” She’d thought they’d already agreed to this. She’d spoken to Harry and he’d agreed, but had he fully understood? Maybe he hadn’t realized she was doing anything more than trying to offer false hope.

Harry’s eyebrows drew together in confusion as he looked back and forth between the adults. “I- okay? I didn’t know that was really an option. Professor Dumbledore always said I had to stay with my aunt and uncle during the summers.” 

They were making a bit of a scene now, which Vernon had clearly noticed, since his eye was starting to twitch. Harry took just a hint of delight in that.

“Dumbledore said it wasn’t an option, Harry,” Sirius cut in, sounding angry, “but apparently someone went around him.” He shot another glare at Natasha. “Harry?” Sirius got down on his level, reaching to brush some hair out of his eyes, and lowered his voice. “Be careful. I’ll check in on you, pup, but I want as many letters as you can manage. Okay?”

“Okay.” He didn’t have a clue what was going on, really, but he was always glad for a chance to not be at his aunt and uncle’s home. He couldn’t afford to turn this down. He looked at Natasha and pulled his luggage cart and little closer. “Where’re we going?”

* * *

_Britain, 1988_

The year on the run had been horrible. The battle had been worse. Natasha had helped where she could, but this was on him and he and the whole world knew it. Killing people though… being surrounded by death, watching those he loved screaming and falling and not getting back up to protect him, walking to his own ensured death… Coming back to a room of dead bodies and mourning family, many of them rightfully blaming him even though they tried not to show it… It had been too much. Far too much for anyone, let alone a seventeen-year-old boy. 

And then. And then after all of that... Then came the press.

Harry had locked the doors, blocked the owls, and hidden away in his mum’s flat, sobbing into her shoulder like a child. “I can’t- I c-can’t do it. I can’t, Mum, please don’t make me face them. I can’t look at- at a-anyone. It’s all my fault and they- they won’t leave me alone and I don’t know what to do and I just want to live my own life and be normal for a _second_ I can’t handle this!”

His distress cracked a window and Natasha gathered him up even tighter in her arms. “Sh. Sh, Harry, solnyshko, you don’t have to worry. I’ll take you away from this place and you’ll never have to see anybody here again, if you don’t want to. Nobody will hurt you again. It’s over. We’ll go to America tomorrow, hmm?”

* * *

_Washington DC, 1988_

“Alright, John. What day were you born?”

“May second,” Harry answered with practiced ease.

“Your father’s name?”

“Patrick Sheppard.”

A hefty confidentiality agreement was slid toward him. “Welcome to your new life. I just need your signature right here. Yes, your old one and the new. Wonderful.”

* * *

_New York, 1989_

John was incredibly grateful for the summers of intense tutoring he’d been tortured with by Natasha. Well. Torture is certainly how he’d referred to it to Hermione. But now, in his new life, it meant it had taken hardly any time to finish catching up and send off college applications, sped along by whatever shady government-adjacent organization Natasha worked for. And now, finally, he was on his way. Stanford. All the way across the continent. But it was what he wanted. And probably exactly what he needed. 

“Mum? Tell me again that I can do this?”

“My darling,” Natasha said, holding his cheeks between her hands in the hope of getting a smile (which she certainly did). “You can do this. You can absolutely do this. You are intelligent and capable, and I’ll support you in any way you need.” She patted his cheeks for emphasis before pulling him into a hug. “And I’m _so_ incredibly _proud_ of you.”

She pulled back to look at her ri ~~diculously tall, when did that happen?~~ child and rubbed his arms. “Do you want to talk through anything?”

He took a second to try to be deliberate about his accent and phrasing, putting a hand over one of hers, then said, “I know my test scores were real, but I don’t feel like I’ve earned this. I dropped out of school and it wasn’t like I was learning real chemistry in the dungeons. I barely know the first thing about American history. It’s hard to feel like I’ve really earned my place.”

Natasha’s smile was sympathetic, but genuine. “I know how hard it can be, to feel like you’ve earned a place somewhere, but… you have, H- John. You’ve earned your place here, and you’ve excelled at everything you’ve needed to, and… well, I expect, based on my knowledge of college-aged Americans, you probably actually know just as much as anyone will expect of you. People might think you’re a little eccentric, perhaps, but they’ll accept you without many questions, I don’t doubt it.”

He crinkled his nose at the new name. It was good, but it still felt strange. It would probably take a good long while to really feel like it was his. “It’ll be weird, not having everyone always looking at me, waiting for me to do something they can write home about.”

“Hopefully it will be a good sort of weird. I look forward to not reading about you on the front page of the morning paper. Hopefully, it will be a chance for you to hide from the trouble that has a tendency to find you. You deserve a chance at a normal life, for a change. Just, please, don’t go to every party, all days of the week. Don’t embrace normality _that_ much.” Her tone was clearly teasing, and she beamed at him.

John laughed and nodded. “Sure, Mom. I promise I won’t go to a party _every_ night. Homework first, at least most of the time.” He leaned into her, the position more awkward than it had been when she’d first taken up this role in his life—when they’d been about the same height. The world really did owe him some comfortable normal, after everything. It was just hard to believe he could really have it.

“You think I might get lucky enough to not have any of my teachers trying to kill me for a change?”

“At the very least, these professors are prosecutable in a court of law.”

* * *

_Stanford, CA, 1993_

John hadn’t told Natasha about joining the ROTC and he wasn’t going to. The last thing she wanted for him was more fighting, but after a childhood of being trained specifically for his sense of honor and responsibility and self-sacrifice and after fighting a whole war… He couldn’t not keep learning how to defend himself and others. And, it had been suggested while he was getting his new identity sorted out. Being in the military would provide him an extra level of security, in regards to his identity, and… Well. And, it would give him the chance to fly again.

By the time he graduated with his degree in applied mathematics, he’d almost forgotten that he was hiding it. She was furious when he left for his first deployment, and John was glad for the distance while she calmed down. That was when he sent his first letter to Teddy. His godson was about five now—that was old enough to understand some of this. 

_(-)_

John couldn’t follow orders. He really thought he could, but the second one of his people was in danger and he was told he couldn’t help, he forgot how to care about the chain of command. If he wasn’t so unreasonably good at flying, it would’ve been a much larger problem.

_(-)_

He just wanted to feel normal. That’s all he’d ever wanted, in his life. Normal people got married. Between his top secret missions and his apparent inability to be properly intimate, she divorced him several years later. He was fairly certain she’d been seeing someone else for the majority of the time they were married. He couldn’t quite find it in him to care about that either. Normal people got cheated on and divorced too, he supposed.

* * *

_2003_

John went in after Lyle. He wasn’t supposed to. It was stupid. But Lyle was his. He’d never loved someone more and he couldn’t leave him to die in the desert, no matter the consequences. 

The consequences were pretty severe. John was transferred to McMurdo, where he became a glorified flying taxi driver for every visitor to Antarctica. 

After a while, maybe it wasn’t really so bad. At least there wasn’t any sand.

* * *

_Antarctica, 2004_

John knew there had been a bit of an unusual buzz around Antarctica the last few months. He’d been transporting scientists and archeologists and military back and forth and mildly alarming rates. But whatever it was, it was classified, and he hadn’t gone looking. Not even when he’d had to fly in a general—a general who’d looked at him like he’d admitted to eating puppies when he’d said “I kinda like it here.”

He hadn’t expected to ever really get a look at what they were doing, but after their surprising encounter with _something_ , complete with evasive maneuvers and rough landing, plus running away, which was more excitement than he’d had in months, he was left with less supervision than he probably should’ve been. The hurried “Hey! Don’t touch anything!” hadn’t been quite enough to get him to stand still and wait in the middle of everyone rushing around.

It only took a couple minutes to wander in far enough to hear, “The second I shut my eyes, I could see i’. I felt this power I’d never had before. I had it dancin’ all across th’ sky. It was magical, it really was. I mean… Well, they’re lucky. I don’ know where it came from. I jus’ tried to concentrate, and th’ drone shut itself down.” That was certainly enough to draw him in a particular direction.

“So _you_ were the one.”

“Me?”

“You’re the one who fired that thing at me.”

“Look, we’re doing research, workin’ with technology that’s lightyears beyond us, and we make mistakes. I’m incredibly, _incredibly_ sorry.”

“Well,” he responded, feeling more than a little awkward now that his joking anger had resulted in a genuine apology. “Next time, just be a little more careful, okay?”

“That’s what I said.”

“What the hell was that thing, anyway?” And then John was getting more information than he’d ever really expected.

“You mean the drone? The weapon th’ Ancients built to defend this outpost.”

“The who?”

“You _do_ have security clearance t’ be here?”

“Yeah, yeah,” he agreed dismissively. “General O’Neill just gave it to me.”

The other guy looked surprised and intimidated, but he didn’t stop talking. “Then you don’ even know about the stargate?”

“The what?”

John stepped up onto the platform as they talked, hands in his pockets to obey the order not to touch, even as he circled the chair. It felt… Well, it felt like a magical artifact. A powerful one. Hogwarts-level powerful. And it was welcoming as hell, though he was also wary of it. He had no clue how a bunch of mon-magical scientists and military people had found something like this or what they might be studying it for. Could they tell it was magic?

“We think the gene was used as a sort of genetic key, if you will, so that only their kind could operate certain dangerous or powerful technologies,” Beckett continued, patting the chair before stepping away.

“So some people have the same genes as these Ancients?”

“The specific gene is very rare, but on the whole, they look very much like we do. In fact, they were first. We’re the second evolution of this form, the Ancients having explored this galaxy for millions of years- Major, please don’t.” And the doctor was moving back toward him as though to stop him.

But John wasn’t going to be stopped. He’d circled the chair, he’d gotten a feel for it, and he was certain it wasn’t dangerous. At least not to him. It was like it was calling him—like it wanted him to sit. And John was bored and curious and very curious about the whole thing, even if genetics and biology had never been that interesting to him. “Come on,” he said, already touching the chair and moving to sit, “what are the odds of me having the same genes as these guys?” Very likely, he already guessed from the way he was being called to, which gave him even greater concerns about possible connections to magic. And then the whole platform lit up and the chair leaned back and he felt a huge rush of power—as though the chair was just waiting for him to give an order so she’d have a chance to help him. It was almost intoxicating.

Beckett appeared to be speechless, mouth agape for a long moment. “Quite slim, act’ally. Dr. Weir!” he called, sounding worried now. “Don’t move!”

John didn’t move. He was in so much trouble. Lord knew where they’d shove him now. Dishonorable discharge for sitting in a chair? That would be just his luck.

A whole mess of people came running. Three more scientists wearing different colors and the general. “I said don’t touch anything.”

“I- I just sat down,” he tried to protest.

The scientist in the orange jacket interrupted. “Major, think about where we are in the solar system.”

John followed the order and the air around him lit up with an illusion of stars, not too different from the ones he’d occasionally interacted with on cloudy nights for Astronomy as a teenager, though the labelling was different. “Did I do that?”

_(-)_

John was put through a series of tests with the chair, bringing up all sorts of ~~illusions~~ holograms. He even briefly lit up one of the drones. It was magic. There was no longer any doubt about that—it was more intuitive than the Room of Requirement and it felt _amazing,_ the chair responding to his every thought and leaving him feeling on top of the world. But he’d be in enough trouble with the non-magical government for touching this thing without orders, even if McKay had looked like he was about to piss himself with excitement as he watched the ease with which John followed his instructions. He didn’t need to be in trouble with the magical government too for letting himself be experimented on. He told Dr. Weir ‘no.’ Gently, maybe. Beating around the bush. But that’s what it was and they both knew it.

Soon enough, he was back in his helicopter, doing his job. General O’Neill didn’t seem inclined to make this easy on him.

“This isn’t a long trip, so I’ll be succinct as possible.” He gave John an unimpressed look.

“Well, that’s pretty succinct.”

“Thank you.”

“I told Dr. Weir that… I’d think about.”

“And? So? Well? _What_?”

“All due respect, sir, we were just attacked by an alien missile. Then I found out I have some mutant gene? Then there’s this stargate thing, and these expeditions to other galaxies.” He shook his head.

“Y’know, this isn’t _about_ you, Sheppard—it’s a lot _bigger_ than that.”

“Right now, in this second, whether I decide to go on this mission or not seems to be about me,” he retorted. He was starting to lose his will to refuse.

O’Neill rolled his eyes. “Let me ask you something. Why’d you become a pilot?”

“I think people who don’t want to fly are crazy,” he answered quickly and easily. That was the truth. He’d loved flying since birth, as far as he could tell, even if he’d forgotten for a while during his unfortunate youth.

“And I think people who don’t wanna go through the stargate are equally as whacked. Now if you can’t give me a ‘yes’ by the time we reach McMurdo, I don’t even want you.”

John had a hard time stamping down his smile. That was awfully juvenile manipulation, but. Well. It might be working. That was basically an order.

He said ‘yes.’


	2. Chapter 1 - A Galaxy Far, Far Away

**Summary for the Chapter:**

> This chapter takes place during SGA episodes 1 and 2, Rising.

**Notes for the Chapter:**

> I got more than a little annoyed by the fact that these folks went to another galaxy, where the human population had had no contact with Earth except through the Ancestors, went out to explore without a linguist, and then the first people they ran into spoke English. And they didn't even throw in a single-line explanation like Atlantis translating for them. Nothing. So. It was established in canon that Latin is based on Alteran, and these people are mostly ancestor-worshippers who would likely want to preserve the Alteran language, so the universal trade language of the Pegasus galaxy is something similar to Latin. I am bad at languages and just used google translate, but we can chalk that up to John not having spoken Latin in a while and the Athosians having ten thousand years of language drift to deal with.

_Stargate Command, USA, 2005_

John was underground, which was one of his least favorite places to be, surrounded by marines and politicians and scientists, everyone speaking languages he didn’t know. He’d even spotted a team of Russian military _something_. And everyone was rushing, which made everything even more stressful. But he’d packed his one bag, sent a letter to Natasha to let her know he was being transferred and everything was super classified, and now he was really committed. He was going to another planet. Or a spaceship, maybe? The details were fuzzy, but there was a very good chance that he’d be leaving Earth. 

There was also a large chance that they wouldn’t be able to connect and they’d all have to wait for more information to try again or that they’d give up. For some reason, imagining that made him more anxious than picturing himself travelling to another galaxy and never being able to come back home.

Because that was a possibility too—not being able to come back.

He was surprisingly okay with that. _Worryingly_ okay with that.

John gathered in the gate room with everyone else, staring at the giant alien ring with open curiosity. He hadn’t really understood what the scientists had told him about it, but it was interesting all the same, especially since if he focused, he could feel a bit of magic around it like he could the chair. He tore his eyes away when Dr. Weir started speaking. “We’re about to try to make a connection. We have been unable to predict exactly how much power this is gonna take, and we may only get the one chance at this, so if we’re able to achieve a stable wormhole, we’re not gonna risk shutting the gate down. We’ll send in the MALP robot probe, check for viability, and go. Everything in one shot. Now, every one of you volunteered for this mission, and you represent over a dozen countries. You are the world’s best and brightest,” or a magical person pretending not to be who can turn on the alien magic technology, “and in light of the adventure we are about to embark on… You’re also the bravest. I hope we all return one day having discovered a whole new realm for humanity to explore, but as all of you know… we may never be able to return home. I’d like to offer you all one last chance to withdraw your participation.” Nobody moved and John looked around in amusement. At least he wasn’t the only one who was worryingly okay with this. They were probably _all_ insane. “Begin the dialing sequence.”

Showtime. John watched at the alarms sounded and the inner ring of the gate began to spin, but he didn’t get to enjoy the moment.

“Let me make myself clear, Major. You are not here by my choice.”

“I’m sure you’ll warm up to me once you get to know me, sir,” he responded dryly. 

“As long as you remember who’s giving the orders.”

He really never had been good at that, but what were they going to do in another galaxy? Court marshal him? Maybe if they got back home, but that was a problem for another day. He could at least try to be good for now. 

John’s resolve to play nice lasted about two seconds. “That would be Dr. Weir, right?” He smiled pleasantly when Colonel Sumner turned back to glare disapprovingly. 

A big woosh of what looked like water burst out from the gate, then settled into a rippling, vertical puddle. Everyone around him burst into applause and he joined in. That was, admittedly, _very_ cool. 

The robot was steered into the event horizon, and they waited.

And then they were done waiting. “Let’s go people; we don’t know how much power we’ve got! Security teams one and two-“ John tuned out Sumner and let himself enjoy the moment now as they all grabbed their things and got in position to move through. 

Before he knew it, he was in front of the event horizon. “What’s it feel like?”

“Hurts like hell, sir.”

John believed Ford more than he had anyone else in that moment, but he took a leap of faith, and then he was experiencing a rush of biting cold, and then he was somewhere else. It wasn’t too much different from apparation, in terms of pain, though it took forever by comparison. Probably just because their destination was forever away.

_Atlantis, Pegasus Galaxy_

He kept walking on the other side, as they’d been ordered to, but with each step he took, more and more lights turned on. He could feel systems activating. He could feel something pushing at his pathetic occlumency shields, and, with another leap of faith, he let them down. Then he was being _greeted_. This city was more alive than any place he’d ever been in. He couldn’t do much more than stare at everything in wonder. He’d thought, at eleven years old, that stepping into Hogwarts had been the moment he’d found his true home. If pressed, he might’ve said that he still felt that way, even a few minutes ago. Now, he knew that he’d had no idea what he was talking about. 

It was only when he realized Dr. McKay had followed him up the stairs that he tuned back into the real world. “The lights’re coming on by themselves,” he lied.

McKay started poking at what looked like consoles or control panels and John distractedly kept watch as the gate finally closed behind the last of the expedition.

Another panel of lights turned on and he held up his hands when Dr. Weird turned to look at him. “I didn’t touch anything.”

“Relax, Major. It’s like the entire complex is sensing our presence and coming to life.” 

No. No, Atlantis was sensing their presence and she was _singing_.

“This has gotta be the control room. This is obviously their version of a DHD.” 

John smiled. If the scientists were figuring things out without the singing, then it probably wasn’t something he needed to share for the moment. “Oh, obviously,” he agreed.

He had enough presence of mind to follow Dr. Weird when she was called down by the colonel, and then he was staring out a window at part of the rest of the city and the ocean around them. Now that he thought about it, he could feel the pressure of it being held back by some kind of warding. Or a forcefield, as McKay said, coming up behind him again. Aliens. This place had been built by aliens, not wizards.

John followed again when Dr. Weir was called to look at something else, and as he listened to the hologram talk about the history of the city, he felt her affirming it in his mind, emphasizing the despair of the great siege with sad, longing notes. He felt her overwhelming grief when the hologram spoke of the remaining people returning to Earth, then she tried to cheer him up, expressing her joy that she was no longer alone. 

It was an enormous effort, keeping his face neutral through it all. 

Another scientist came in and spoke urgently to McKay and they were all informed that power levels were dropping and nobody knew why. Atlantis felt confused when he tried to ask her about it. He tried to ask her to shut things down, next—to turn everything back off—but although it was clear that she heard him, he wasn’t sure she really understood. All she did was try to soothe his fear, which was a little disconcerting.

Did that mean she didn’t believe there was anything to worry about because there was a failsafe in place they just couldn’t see? Or that she couldn’t see that there was a problem? John sat and tried to impress upon her how important it was that she cooperate so they could be safe, but although their feelings were shared with no problems, he was beginning to suspect that there was some kind of language barrier. Maybe now was the time to come clean, but he’d spent his whole adult life hiding everything about his former identity. How much could he safely say now? He wouldn’t have the first clue how to talk about any of it. If he didn’t explain to their satisfaction, would they blame the gene they’d found and let it be or would they poke and dig until he revealed something they really shouldn’t know?

Still not sure what to say and frustrated that his attempts at communication with Atlantis weren’t going as well as he’d hoped, John suggested evacuation. “Maybe somewhere in this galaxy.” If they couldn’t go back to Earth, maybe they could still survive by going to a different, drier planet. That’s what the stargates did, right?

And they accepted that. In less than a minute, he was being shoved back through the gate as part of the Colonel’s exploration team, hoping to find somewhere safe.

The last thing John felt from Atlantis as he stepped back through the gate was distress. She might not have a clue what he was talking about or why he was worried, but she could tell he was leaving and she was clearly very upset about that. 

The gate shut down behind them and then he was alone in his mind again, his head suddenly aching. Evacuation felt like a _terrible_ idea, now.

* * *

_Athosia_

John lowered his darkvision goggles and stepped warily into the forest with the rest of the group. It was just their luck that they’d run into a couple children in monster masks when they were on the look-out for actual monsters.

_“Placet! Nolite Nocere Nobis!”_

John looked quickly at the other soldiers, trying to see if any of them looked to be trying to figure out the language. Why hadn’t they brought one of the anthropologists? What were they supposed to do with a couple kids who didn’t speak English? Or, most likely, any language at all like ones they’d encountered before.

At least an adult came running fairly quickly. _“Placet!”_ He help up a hand, placing his body between them and the children, and they all lowered their weapons. Slowly, obviously trying to appear calm after a scare, the adult stood, helping the children up and gathering them close again. Then he gestured to himself. _“Halling.”_

“I don’t know what that means,” John said, hoping someone else would have some idea what to do.

“It’s his _name_ ,” the Colonel said, a bit harshly, considering. Although John did feel like a bit of an idiot, because that seemed obvious now.

“Oh.”

Halling looked as puzzled now as John was feeling, at least.

“Halling, uh. It’s nice to meet you.”

_“Et commercia quidem mihi est hic?”_

John furrowed his brows. That… sounded familiar. He’d been sort-of speaking an archaic form of Latin since he was eleven. He was a little rusty now, and none of what he’d actually used or was still using was conversational, but Hermione had decided they were all going to learn it properly in their third and fourth years, so he still knew enough to string together a sentence if he had some time to think. He really wished he had more time now.

“Uh… er. Okay,” he started, with a look of intense concentration. “Uh, _Venimus in… occursum adventus tui… cumque… negotiari._ ”

The other soldiers looked at him like he’d just gone insane, but Halling tilted his head a little and watched John carefully for a moment before nodding.

John _beamed_. Maybe he hadn’t actually understood, or maybe he’d said something, but it had come across as meaning something entirely different, but _something_ had been understood, and that was huge.

Halling looked amused for just a moment before relaxing enough to kneel down and address the children. _“Quot ego dixi vobis non ludere in tempora post silvam et in tenebris? Salvum me solum laeti sunt.”_ He pressed his forehead against one of the children’s for a moment, then stood again and turned back toward John. _“Teyla ad te voluerit.”_

John actually thought he understood some of that, and it made sense, which meant there was a greater chance he was actually getting across what he wanted to too.

“What was that? What were you two saying?” the colonel demanded roughly.

“Ah, he, uh, asked if we were here to do business, I think. Then I tried to say ‘yes,’ and that we were here to meet them and trade, but… Honestly, sir, my Latin’s a little rusty. It’s a dead language, you know, and I have no idea why these folks are speaking it. How would they even have known about it?” He cleared his throat awkwardly, then continued, “But he said something to the kids about playing and dark and then said something about a meeting.”

Sumner gave him a confusing look, then nodded. “Alright then, guess we’re headed with them. Keep alert.” He set two of their group to watching the gate, then gestured for the rest of them to stick together.

Halling watched them for a moment, then, when John nodded at him, said, _“Veni,”_ and set off through the woods. They all followed, all the way to a little village, and John got some practice with the language with the kids as they walked.

 _“Quid enim personam gerit?”_ one of them asked.

 _“Haec?” This?_ John took off his dark vision goggles and the boys nodded. _“Nam… cum in tenebris.” For seeing in the dark. “Vide, experiri.” Look, try._

They exclaimed excitedly as they looked through it and John smiled indulgently, wondering for a moment if Teddy would be just as enthusiastic about all his non-magical military gear, which he found so common now.

_“Non possum ego sum?”_

_“No. Quid enim… est quam persona circumdatio?” No, you can’t have it. What’s the mask you’ve got on?_

_“Haec? Larva. Wraith.”_

_“Wraith? Quid est?” What’s that?_

_“Tu non scis? Quae ex mundo veniunt facere?” You don’t know? What world do you come from?_

_“Ire non possumus?” Can we go there?_

_“Me paenitet, neque. Est procul.” I’m afraid not. It’s in a galaxy far, far away._

Eventually, they were lead into a large tent and they met with who John had to assume was the leader of the village, or at least someone important. It was a bit of a rough start, but John stumbled through some awkward greetings, rambled about himself when she said they were strangers, and made her smile. Then they all joined her and her people for tea. It was nice. He almost forgot, for a moment, about the burning emptiness in his head where Atlantis had so recently made herself at home inside him. And about how much his new CO clearly didn’t like or trust him.

John bonded a bit with Teyla, the leader, and before long, she was taking him to see something important, John growing more confident in his communication by the minute. When a flash of silver caught his eye on the ground and he returned her lost childhood necklace, he felt that they were starting to cement a real friendship. He hardly felt the spark of magic in the jewelry, not thinking anything of it, since she said it was already hers. Clearly, it wasn’t a curse. And the history she’d showed him on the walls of the ruins was enough to help him start to connect the dots between the Ancients’ great enemy and the Wraith, which, as Teyla told him more about them, were sounding more and more like just organized vampires with spaceships. Maybe this trip had been worthwhile and they’d be able to safely stay here until they figured out how to save the city. 

His hopes were dashed when the wraith came.

There were space ships and illusions and it was everything scifi-horror movies had prepared him for aliens to be. He felt like he was back in the war, running from sadistic wizards on brooms who could toy with sanity and shoot spells from above, but his wand wasn’t easily accessible, and the idea of letting go of his gun to get it was deeply unappealing. But Teyla was taken. And then the colonel was. And suddenly he was in charge. 

He had the presence of mind to order Ford to look at the gate address as the ships left, then got his wand out of his pack and into an arm holster before children started begging for his help. He couldn’t leave these people alone.

_Atlantis, Pegasus Galaxy_

He helped gather as many people as they could find alive and, although he knew it was dangerous, they had nowhere else to go. They returned to Atlantis. And then he couldn’t regret it at all because there was her singing again. She was distressed by everyone’s obvious worry, but mostly, it seemed she was happy that he was back.

Unfortunately, he didn’t have time to enjoy it. The shield was apparently seconds from failing, and he set Jinto, one of the children, to dialing a safe gate address, but it wasn’t fast enough. In a last desperate attempt to keep them all safe, he tried to express the problem to the city in Latin instead of English. 

_The shield is failing and you’re going to be flooded._

Miraculously, shockingly, unexpectedly, beautifully, Atlantis understood him. And she rose.

They were pushed up out of the ocean and they settled on the surface and they all, somehow, survived. 

Atlantis sang. 

Jinto shoved his way into John’s arms and he let himself take a moment to just hug the kid and watch the water slough down the windows of the tower. He let himself breathe.

**Notes for the Chapter:**

> Thanks for the feedback and encouragement! I have decided to continue, but I'm still making no promises about finishing. Please keep letting me know what you think, though, and feel free to make requests about what specifically, you'd like to see me look at.


	3. Chapter 2--Guess This is Home Now

**Notes for the Chapter:**

> This finishes out covering the events of episode 2, Rising. Now that I've covered them getting settled, I'm going to step away from the main events a little and focus more on behind the scenes happenings in future chapters, though I may still cover interesting parts of canon to show John's thoughts and any changes that might happen because of magic and whatever else.

They were safe. The city had risen and was now settled comfortably atop an ocean. It was big enough that they couldn’t even feel the motion of the waves and the atmosphere was breathable. Considering their panic only a few minutes ago, they were doing really well.

Less fortunately, there were no landmasses in sight, which made them a fairly obvious target, they couldn’t reactivate the shield, and John was now, somehow, the ranking military officer on this expedition of scientists, plus their new refugees. And they had no great way of organizing a rescue mission yet.

When McKay finished laying out their situation and John had finally started to get used to Atlantis back in his mind, he asked how soon they’d have an address to go to. McKay had dithered, but the look of shock and confusion on his face when John had said, “Seven hundred twenty, yes,” was a bright spot of joy. He thought he might really come to like McKay, if given the chance. 

“Take away the coordinates you can’t get a lock on… and that’s your one. And when you find it, send a MALP.” McKay seemed to want to say something more, but instead, he just awkwardly nodded, then walked away. Yeah, no matter how odd it felt after all this time, he could be in charge. This was going to be fine.

Until Dr. Weir tried to shut him down. “Major? A word.”

“Let me guess,” he started, once they were situated on a balcony. “You’re not gonna let me rescue my people.”

“Major, you don’t even know if they’re alive.”

“Y’ _don’t_ leave people in the hands of the enemy!” No, he could do this too. He could fight for his people. For Jinto’s father and his CO and everyone else who had been taken. “And the fact that we are having this conversation in private lets me know that you know _damn_ well that it’s wrong. _And_ it will totally undermine your leadership, so as ranking military officer-”

“All right, just shut up, and listen to me for a moment, alright?”

John froze, as he’d always done when startled or confronted with something upsetting, but he shook it off in a moment and reluctantly let her go ahead.

“Come on, what d’we know about the Wraith? One of the few things we _do_ know is that they are the enemy that defeated the _Ancients_. When we first began to use the Stargate we found on Earth, we got ourselves into serious trouble. Why?”

For a moment. “I don’t need a history lesson,” he interrupted.

“Because the people in charge didn’t consider the ramifications before they reacted!”

“They took our people! How am I supposed to react?”

“And we’re defenseless! You said so yourself. How do you know going off on some half-assed rescue mission isn’t gonna bring them all right back here to our doorstep?”

“Maybe it will. But it’s the _right_ thing to do.” He’d spent his whole life doing the right thing instead of the easy thing regardless of consequences. He wasn’t about to give up on everything Gryffindor had taught him now. “Why? _Because it is_!”

“John…”

“If we’re not gonna do this—and I mean _right now_ —then let’s just turn tail and pack up. Because they’re coming.”

“You don’t know that.”

“Our people are in the hands of the enemy, Doctor. Do you know what that means?” It meant they were dying, being tortured. It meant that John had failed them, but he wasn’t going to let it go, just like he hadn’t let it go when his people had been taken or left behind before. Not ever. “It is just a matter of time before the Wraith figure out that this is the base of our operation.”

“I just need more information. I mean, who knows? Maybe we could negotiate a peaceful-”

“Peaceful? Are you _kidding_? We weren’t there for more than a few hours before they showed up.”

“Is it possible they came _because_ of you?” He knew she didn’t mean him personally, but he’d probably never let go of the guilt that had followed him his whole life—that he was the reason the people around him got hurt. It touched a nerve. He clenched his jaw and looked away, but gave a half a nod. “And that one of these people you brought back here with you tipped them off?”

“It’s _possible_ ,” he admitted grudgingly, hating himself for considering it.

“See, that is exactly the kind of snap decision I am referring to!”

“They’re not all bad people. You know, if we’re gonna stick around here, we need friends.”

“Okay, I see your point. Now, you see mine. I will not authorize a rescue mission unless I’m sure there’s at least a remote chance of success. I’m not sending more good people, including you, to their deaths.”

That was… a refreshing perspective. Normally it was just writing people off as acceptable losses and saying a rescue wasn’t worth the effort. But this way… he’d just have to make a plan and prove he could do this. “Okay.”

* * *

John went straight to McKay and whoever else had been corralled to help with finding the address from the symbols they’d seen. This was important. Once they could get a look at what they were going into, they could make a reasonable plan to get in and out. 

Most of the possible addresses just wouldn’t connect, as predicted, but they managed to get a lock on one of them. They waited until Dr. Weir could come see before sending the MALP, but it was in space, which was both unexpected and interesting. Had the Wraith put it there or had the Ancients also used some kind of ship in combination with the gates? They certainly couldn’t go through the gate after their people on foot.

That was going to delay things.

He didn’t even acknowledge her apology, too deep in his head as he tried to come up with ways to get their hands on a ship. He was just about to try directly talking to Atlantis again (though he was less sure now than he had been an hour ago that she had actually understood him and the city hadn’t just risen as an automatic failsafe) when McKay pulled him back to the real world with an invitation to join him.

John went.

And there were space ships, perfectly designed for the gates. Yeah, putting them in space was definitely the Ancients’ idea. He was going to get to fly a _space ship_. If not for the circumstances, that might have been the greatest gift he’d ever been given.

It didn’t sing the way Atlantis did, but it had a pleasant hum of its own, a lot like the chair back on Earth. It came to life under his hand and obeyed his commands about as easily as his old Firebolt. With a little experimentation, it even turned invisible, and he’d loved the feeling of being unseen and therefore safe he was eleven and had first experienced it. Yeah, this was a plan.

He convinced Dr. Weir and then it was just a matter of gathering a couple soldiers and playfully bickering with McKay and Ford over the name. He and this Puddle Jumper had a lot of good times ahead of them.

* * *

It was like threading a needle in the most exhilarating way possible. John flew them through the gate, turned on the cloak, got them navigation and a cool life signs detector, and he was just tired and excited enough to let his experience with magic come out enough to breathe, joking with Ford abut getting the ship to make him a turkey sandwich too, since it was so good at reading his mind and responding to his needs.

They were going faster than he’d ever gone in his life and it felt like nothing more than riding a breeze and it was… truly, really amazing.

When it was time to land, that joy faded significantly. He fiddled with the handheld detector until he got it to turn on, took a second to appreciate how Ancient technology didn’t break if he didn’t concentrate on keeping his magic in check, and pealed off with Ford, leaving everyone else with the ship for the moment. As they walked, he kept clenching his fist, just to feel the arm holster and his wand and continually reassure himself that they were there.

It was shockingly easy to get in. It wasn’t even really difficult to find the prisoners. It seemed like the whole place was abandoned. But without Sumner, they wouldn’t break out just as quietly.

Determined, John split up once again, leaving Ford to break out the prisoners they’d found and ordering the men back at the ship to create a distraction as he went in search of their CO. He could do this, but with vampires… well. He’d rather not have to remove any memories. He might need more than his gun and that would be easier with fewer witnesses.

He moved as quickly as he dared, checking the life signs detector frequently, but he wasn’t fast enough. When he heard the Colonel scream, he stopped pretending to keep up appearances at all, letting go of his gun to grasp his wand instead. Then he ran.

It took far too long to figure out how to move between levels, then he had to try to be a good soldier and watch from a distance, but he didn’t last long. He shot out a powerful burst of magical sunlight, which should have momentarily incapacitated a vampire. Unluckily enough for him, these ones didn’t play by Earth rules. All it did was draw their attention. He tried stunners next, and that worked better, but they shot back and didn’t stay down and the Colonel was still screaming, the Wraith hissing at him in a language he couldn’t even begin to comprehend, her hand on his chest. And she wouldn’t go down at all.

Colonel Sumner was clearly losing this battle—the Wraith taking his life to protect herself, somehow, and as he looked on with horror, Sumner met his eyes. Then nodded.

John’s throat constricted, his heart tightening, but he couldn’t let this happen. Horrified he cast the killing curse. He should’ve used his gun, but who was going to tell anyone? He couldn’t bear to add to the pain this man was already clearly experiencing by ripping through him with a bullet. No, a quiet, careful _avada kedavra_ provided a quick and painless death, which the Colonel had more that earned, and it at least deprived the Wraith of the last of its meal just as well as any other method.

Colonel Sumner collapsed and the Wraith finally turned to him, looking furious. John didn’t feel the one coming up behind him.

As soon as he came to, painful prickling making every second of reawakening more uncomfortable, he was being interrogated, the hissing, growling language they’d been speaking before twisting to something resembling English as it forced its way into his head, more violently than any Ancient technology did.

Ford, thankfully, came to his rescue.

The Wraith dead, he relaxed for just a moment, but then it was like they were back in that horror movie, life signs popping up out of nowhere all around them and them rushing to escape. And through that, he had to attempt to summon his wand without Ford noticing. He was really far too tired for wandless magic, but… It flew to him and he played off catching and stowing it as a stumble and they kept on running. And running.

It was a long, dangerous, exhausting journey back to the jumper and they all squeezed into it, breathing heavy and still dodging enemy fire. And then they were up and moving and John had a hurried, shouted conversation in broken Latin with the Athosians, then they had to do something even more dangerous. He’d thought flying a fighter jet while under fire was difficult—that dueling on brooms was hard. But space battle? That was something else entirely. If the jumper hadn’t been so unbelievably intuitive, they all would have died. As it was, they took damage and they barely avoided slamming into the interior wall of the tower once they were through the gate.

“ _Ladies and gentlemen, welcome to Atlantis,_ ” he said breathlessly to the Athosians as he eased them up into the bay, now feeling every heavy thump of his heart within his chest. “ _Please remain seated until the ship has come to a full and complete stop._ ” The reference might have been a bit lost on them, but it made him feel better.

* * *

“I guess this is home now.”

John looked back at Ford with a smile, still subtly fingering his wand. Atlantis was filled with groups of laughing children, relieved familied reuniting, and excited and exhausted people of their own. She was singing contentedly. “I guess so.”

He toasted to their safety with the champagne sent by General O’Neill and tried not to let himself feel too good about things. He’d lost someone--someone whose responsibilities he now bore. He appreciated the alcohol, but this was no time for getting lost in celebration. He wasn’t prepared for this. He’d killed someone with magic using an unforgivable curse. He’d fought aliens. He’d, apparently, woken up hundreds more of the bad guys. 

But. He had made them a couple friends.

Awkwardly, hesitantly, John returned Teyla’s forehead touch. It was, possibly, the most intimate embrace he’d experienced, fully clothed and in view of other people. It was nice. 

* * *

Sleeping quarters were organized, supplies were rearranged, and John slept. And then he woke, and in the dark hours of whatever passed for early morning on this planet, he wrote a letter home, though he’d never get to send it. 

_Mom,_

_I don’t know what I’ve gotten myself into. I didn’t come here expecting to be military commander, but we’ve lost people and we’ve gotten involved in a fight for our lives and I know you hate how I do that. We saved people too, but I killed my CO. It was necessary. It was the right thing to do, to give him a quick death, but I killed him. And I wanted him dead or it wouldn’t have happened. I’m not sure how I’ll come to terms with that._

_I wish I was back at home._

_I’ve never run a military base before. I’ve never been asked to be in charge of civilians as well as soldiers. Not since… you know._

_There’s not even any snakes here to talk to._

_But I’ll be fine. I’m going to keep them safe, I promise. As safe as I can manage._

_John_

Better than journaling.

Then he got up, brushed his teeth with no running water since the scientists hadn’t figured out the plumbing yet, and got pulled into a meeting with several of the linguists and anthropologists to talk about working with the Athosians to set up lessons in their universal trading language. Apparently it had gotten around that he was the only one who had been able to really communicate with them so far. Latin gave them a good place to start, but they all needed to figure out how to talk to the people of this galaxy before they could confidently go back out there to trade for food and supplies. Then his soldiers needed him to provide directions and listen to reports and complaints, then Elizabeth needed an update, then McKay needed his input. 

At least he didn’t think he’d made too big a fool of himself yet.

**Notes for the Chapter:**

> Please keep commenting! All your messages are greatly appreciated and hugely motivating, and the last thing I want for this story is to lose motivation. Thank you to everyone who's already bookmarked and subscribed and left kudos. You guys mean the world to me!


	4. Chapter 3--Activation

**Summary for the Chapter:**

> This chapter takes place during and around the episode "Hide and Seek".

**Notes for the Chapter:**

> I've stretched out the timeline a little, because the amount of time it took them to get set up and start the ATA gene modification in canon felt unrealistic. Also, anywhere in canon where Athosians are talking to people, feel free to picture linguists or archeologists or someone acting as a not-great translator. I'm keeping things John-centric, but if you all are interested, let me know and I might do a one-shot or two focused on stuff like that.

Chapter 3: Activation

It had only taken two days for the issue of only having a handful of people who could turn things on to become a big enough problem to pull John away from his other responsibilities. Beckett had terrible bedside manner, but he was a great researcher. 

“Y’ don’t have t’ be such a baby,” the doctor teased, pressing another cotton swab to the crook of his arm. John felt terrible for the mice that had been jabbed alongside him. 

“Yes, sure, that’s what’s happening here. Couldn’t have anything to do with the way you’ve confiscated half my blood. On Earth, doctors gave out cookies in exchange for large quantities of blood.” He laid back on the bed without a hint of shame. 

He spent his mornings in the makeshift infirmary, soldiers and Elizabeth sometimes coming to him for the most important issues, then he went and did training and mediating and endless unnecessary paperwork in the afternoons. He’d come to peace with what was happening after the second day. If Beckett discovered what made him magical—if his proposed gene therapy meant other people started developing magical abilities—they’d deal with that when it came. As of now, they were cut off from Earth, threatened by aliens who wanted to eat them, and short on supplies. He just couldn’t afford to spend the energy worrying about the Statute of Secrecy.

After another couple days of listening to Beckett work, John had decided that the others on base with the gene were squibs. Some of them might even know it, but everyone in the wizarding world who cared to look into it knew that squibs—people who couldn’t do magic, but could see and interact with magical creatures and places—could be born into muggle families the same as muggle-born witches and wizards. They made up a large chunk of the ghost-whisperers, mediums, fortune-tellers, and other mystics in the muggle world. Oddly, a bunch of people on base who weren’t squibs or magic-users had the gene responsible for it—the gene passed down by the Alterans interbreeding with humans—but it just wasn’t active. Maybe that was how muggle-borns and squibs from non-magical families happened.

It took a week, all said, for Dr. Beckett to be ready to test the gene therapy on people with the dormant gene. He probably should have stayed around and watched. Seeing Rodney interact with other people was always incredibly amusing all on its own, and John had already taken to just sort of hovering near the science labs just to be around him, but he really ought to be there in case Rodney got the therapy and immediately started blowing things up. He couldn’t though, since he was dragged away by a marine to approve another corridor of cleared living quarters. He’d just have to deal with any fallout later. 

Luckily, Rodney sought him out right after the therapy to show him a fun new toy. Even more luckily, he didn’t seem to be having any violent magical problems yet. And even more luckily than that, it looked like he was going to get to play with the toy.

“Look, Major, I’m almost entirely sure this thing here is a personal shield. And now, I should be able to turn it on. Care to help me test it?” The scientist grinned and John smiled right back.

“Have you turned on anything else yet, or is this your first shot?”

“Activated a console a couple minutes ago,” he answered excitedly.

“And this thing is safe?” John confirmed. So being repeatedly drained of blood had been worth something after all. Sweet.

“Please. It’s a _shield_. Safest thing we’re going to find.”

“Alright then, go ahead.”

Rodney beamed even more brightly, pressed the device to his chest, and willed it on. And it worked. He hit himself in the thigh, dropped something heavy on his foot, and kicked a wall—a shimmery green force shield cushioned all the blows. “Yes! Alright, c’mon, hit me.”

John only hesitated a second before throwing a light punch. The shield left his hand tingling and it was just about the coolest thing ever. Rodney looked ecstatic. Soon, the two of them were running all over the cleared parts of the tower looking for new ways to test it. Rodney tumbled down stairs, poured boiling water on his leg, and encouraged John to try anything he could think of. When his back was turned, John even shot a stunner at him, too curious to resist. It bounced right off and John got even more excited. It didn’t take much longer to talk him into shooting him in the leg, and it was a short jump from that to shoving him off the balcony in the gate room. 

Elizabeth was visibly exasperated when Rodney finished bragging and her worry had faded, but then both Rodney and John’s faces fell as they realized the device wasn’t coming off on command.

Maybe this was because of the therapy? John had had years of training to learn how to properly control and direct his will, making turning devices on and off as easy as casting _lumos_ and _nox_ , but some of the others with the natural gene had struggled to get Ancient devices to respond right away. Maybe this was just more of that.

John reached for the device, concentrating as thoroughly as he did when casting the most complicated advanced magic, but it didn’t acknowledge him at all. “Just checking,” he said, immediately masking his worry. This thing wasn’t immediately dangerous and Harry had once coached first years from struggling with their first spells all the way to casting a _patronus_ charm. He could do this. After the meeting.

* * *

Rodney went to keep working on the problem and John did his best not to think about it while he focused on security issues and tried not to be too angry about leaving the Athosians in the dark about a lot of their situation and plans. They were civilians and a security risk, but somewhere between running for their lives together and the rescue mission, John had bonded with them, and it hurt to force himself to ignore his instinct to trust.

But there were even bigger problems than that. Rodney seemed fine for the moment, even with the problems caused by the shield, but now Jinto was missing and the city was having power problems again. 

He’d just set off after Jinto, searching along with the other groups, when the power fluctuated again and Atlantis’ song became overwhelming for a moment, filled with fear and confusion. He wanted to help, but she didn’t seem any better informed than any of the scientists or technicians working on the problem, so all he could do was try to communicate to her that they were doing their best and keep focusing on his job. He might’ve killed for some Aspirin, though, when her confusion and other erratic emotions in his head just got louder.

And then he was forced to fall back to deal with a potential wraith threat. If they could just have one crisis at a time, that would be a miracle.

And then, of course, Rodney fainted, and John really didn’t have any time to deal with that until other issues were handled.

Thankfully, Atlantis or something else finally gave them a break and a fluctuation in the communications system let Jinto talk to them so John could at least rush off to rescue the kid and check one problem off the list. And that, even better, gave Rodney a chance to identify the thing draining the power as some kind of Ancient research project. John was _very_ impressed by Rodney’s special kind of crisis-enhanced genius, but if anyone were to try to confront him about his momentary look of dopey pride, he’d certainly deny it.

He’d also deny repeating that look later, when Rodney had managed to get the shield to shut down in an adorable, if exasperating display of uncontrolled magic responding to fear, but then he put it right back on in order to save them all.

* * *

“You’re going to have to help,” he told Rodney later, still gazing at him with, perhaps, slightly too much fondness, considering. “With the language, I mean. You’re one of the people who reads Ancient, and apparently there’s not enough people who do for you to get out of it. Everyone going through the gate is going to need to be speaking Ancient semi-fluently before we can hope to effectively trade for any food or supplies, and what we brought is running out fast.”

Rodney looked up at him disbelievingly and John smiled back, swinging his legs a little from where he was perched on a dead console. “You’ve got to be kidding. The city is only still afloat because of me. I can’t spare a second for doing the jobs of other departments.”

“Maybe, but at the very least, you’ve got to learn to speak it. Reading gives you a head-start, but-“ he shrugged. “I want you ready to go off-world if I need your expertise out there. Who knows what your underlings would do to any useful Ancient tech before they got it back to you.”

Rodney looked outraged at the very idea of someone else getting to the tech before him. John grinned.

City-wide language lessons teaching Ancient to as many people as they could and teaching English to as many Athosians as cared to learn began in another few days. Rodney was sometimes there, which was about as good as John had hoped for.

**Notes for the Chapter:**

> Please keep commenting! Let me know what you liked seeing and what you'd like to keep seeing or what you'd like me to try! Thanks for showing your support!


	5. Chapter 4: Regret

**Summary for the Chapter:**

> This chapter covers S1E4-S1E7.

Chapter Four: Regret

The city was a riot of activity at all hours of the day. Rotating language classes teaching Alteran, English, and Athosian took up part of almost everyone’s day. The engineering teams were spread out learning how systems worked, activating and deactivating things, and doing necessary repairs. The botanists had been busy planting and tending to seeds, carefully setting up and activating a pair of the city’s many greenhouses. And everyone with the gene, induced or not, had been taught the intricacies of manipulating Ancient technology. All of the military with the gene underwent mandatory flight training in the jumpers. And to top it all off, there were self-defense lessons and kitchen duty and patrols.

It was a lot. It was wonderful. 

But they were running out of perishable foods. They couldn’t afford to stay in the city any longer, even if every mission, trade and reconnaissance, seemed to end in disaster. Dr. Beckett was getting plenty of work. And John, unfortunately, was getting all too familiar with the way people looked when scared. 

Really, stuck in the back of a jumper, wedged in a gate with a creepy alien bug sucking on his neck just felt like a logical escalation. The paralysis was just an extra cherry on top. It took more out of him than he was proud of to force himself to come back again after they killed him to remove the thing.

 _Maybe_ there were other things they couldn’t afford to wait on either. John had the awful suspicion that the reason the engine pod hadn’t retracted properly was because none of the people with the modified gene had any of the necessary control over their newfound touch of magical ability to not let emotions interfere with their mental commands. 

It was an extraordinarily fine line between breaking the statute of secrecy to save lives and breaking it to make things easier.

o~o

“McKay.”

“Yes, what?”

“Come with me.”

John wasn’t sure he was making the right choice here, but he and McKay had gotten reasonably close, over a half-dozen off-world missions and watching each other almost die a couple times. And he knew now that Rodney had at least slightly more than squib-level magic. If he was going to tell someone, it should be Rodney, who he already trusted to have his back in dangerous circumstances and who he could keep an eye on. 

They walked out to an empty pier, Rodney grumbling most of the way, and John handed him something vaguely mango-like when they sat down. Then, without any further preamble, John cast a wandless lumos, a ball of soft white light appearing in the palm of his hand.

Rodney’s grumbling and confused questions about the fruit ceased. 

“I’ve always been able to do this. You can’t tell anybody. Do you understand me?”

“What? What is-?”

“I need you to promise to keep this secret before I tell you anything else.”

“I… Wha- _Yes_. Yes, alright.” He didn’t look particularly pleased by his own agreement.

“I think it’s linked to the ATA gene and I think you might be able to do it too. I think it’s why I have so much better control over Ancient tech than anyone else—because I’ve been practicing this since I was a kid. I want you to have my back, McKay, so I want you to have control too. Let me teach you?”

“ _What_?”

John did an exhausting amount of wandless magic that night to satisfy Rodney’s curiosity, and had to remain very firm despite a great number of protests on the telling other people issue. But, even though Rodney didn’t manage to do any intentional magic that night, John thought they’d made progress. In time, he was sure they’d manage something.

o~o

Sometime between the routine of training and exploring and practicing speaking Ancient and the less routine missions to search for food and ZPMs, John found time to continue teaching Rodney magic. He didn’t learn particularly quickly, but it was worth the time for the way Rodney seemed to interact more naturally with the city every day; he even started to hear her song, on occasion. It was worth it for the time he got to spend _with Rodney_. That was worrying, because the last thing he needed right now was a strong attachment, when he _knew_ he’d be pulled off the mission as soon as they got back in contact with Earth. He wasn’t qualified to be the commander of an expedition like this and he’d _killed_ his CO. But he found after everything, he couldn’t put up any of the barriers he should have. Rodney was just such a _good friend_ and John hadn’t had one of those in ages.

They didn’t always have their magic lessons in the same place, which was how they discovered The Game. That only served as another bonding activity, and John was sure it was going to come to bite him later, but watching Rodney’s face every time John accused him of cheating or teased him about the flag… Well. He’d deal with the consequences when they got around to coming.

o~o

And then there was Steve.

John had been trying to get information from him for two weeks before he broke and gave the wraith a name himself. That wasn’t a good sign for his progress, no matter how confident he tried to seem. He’d had prisoners before--he’d even interrogated enemies before—but none of them had been so unphased. It felt like Steve really saw the whole lot of them as no more dangerous than particularly angry bunnies. Steve was hungry, which was something, but they knew so little about how the wraith worked that it was hardly reassuring. John wasn’t even completely convinced that the wraith had souls he could manipulate, and he wasn’t ready to get close enough to a hungry predator who wanted to eat him to find out.

He waited. He joked and suggested and smiled in ways that didn’t come close to reaching his eyes and he let Dr. Beckett run tests and harvest samples and he even let the Hoff run their drug experiments, despite how firmly against the Geneva convention it was. There just… didn’t seem to be any other options. They couldn’t let Steve go and they couldn’t get him to talk and they couldn’t even keep him alive without sacrificing their own people. It was awful. It was almost enough for John to wish he was any good at legilimency. Or that he’d brought along some Veritiserum, though it likely wouldn’t have worked as intended on an alien.

And then Steve died. John knew he was going to, but Steve didn’t die of starvation; he died from the Hoffan drug—the drug John had convinced Elizabeth to let them test. Then the Hoff deliberately killed fifty percent of their population so they could keep killing the wraith. It was horrifying. John had seen war, but nothing like _this_. He’d never felt quite so sickened by his own decisions. 

He’d offered the Hoff good luck, but when they returned to Atlantis, John got drunk on Athosian wine and rested his forehead on Rodney’s shoulder, shaking. He hardly said a word, but Rodney filled what silence was left around the city’s musical concern, and it was comforting.

**Notes for the Chapter:**

> Did you all pick up that hint about John's Master of Death powers? Just a taste for now.   
> Sorry it's been so long, but time is weird right now and I've had other stuff going on. I really can't promise any better.  
> Please leave me some comments! Let me know what you think and what you'd like to see me write about, either scenes in the series that might go differently or moments off-screen you'd like to see happen.


End file.
